biogems.info - gems for bioinformatics

Matsumoto Yukihiro, a.k.a. Matz, visits Biohackathon 2018 !

#	biogem	description	by	version	released	stars	issues	total	7d	90d**)
								downloads	commits
1	bio	Bioinformatics library	BioRuby project	1.5.2	11 weeks	325	13	198520	3	8
2	biodiversity	Parser of scientific names	Dmitry Mozzherin	3.5.1	2 months	26	4	94574	0	1
3	bio samtools	Binder of samtools for Ruby, on the top	Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal	2.6.2	11 months	29	10	67920	0	0
4	sequenceserver	Blast search made easy!	Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.	1.0.11	17 months	135	42	59204	0	13
5	bio gem	Biogem is a software generator for Ruby in	Raoul J.P. Bonnal, Pjotr Prins	1.3.6	4 years	14	12	59169	0	0
6	bio gadget		Shintaro Katayama	0.5.0	22 months	1	1	45245	0	0
7	bio ucsc api	The Ruby ucsc api: accessing the ucsc genome	Hiroyuki Mishima, Jan Aerts	0.6.5	7 months	17	1	41787	0	0
8	entrez	Http requests to entrez e-utilities	Jared Ning	0.5.8.2	3 years	8	1	37346	0	0
9	bio svgenes	Create pretty svg-format images of features, gene models	Dan MacLean	0.4.1	4 years	15	5	36033	0	0
10	bio polyploid tools	Tool to work with polyploids, ngs and molecular	Ricardo H. Ramirez-Gonzalez	0.9.9	2 weeks			32860	0	0
11	biomart	A Ruby api for interacting with biomart services	Darren Oakley	0.2.3	7 years	17	5	32695	0	0
12	bio maf	Maf parser for BioRuby	Clayton Wheeler	1.0.1	6 years	10	36	30191	0	0
13	bio blastxmlparser	Very fast parallel blast xml to rdf/html/json/yaml/csv transformer	Pjotr Prins	2.0.4	3 years	14	1	28951	0	0
14	bio gff3	Gff3 parser for big data	Pjotr Prins	0.9.1	6 years	7	2	28111	0	0
15	bio grid	A biogem to submit jobs on a queue	Francesco Strozzi	0.3.3	6 years	4	...	26722	0	0
16	search biomodel	Interfaces with biomodel search engine	Niall Beard	2.1.6	6 years	1	...	26391	0	0
17	biointerchange	An open source framework for transforming heterogeneous data	Joachim Baran, Kevin B. Cohen, Geraint Duck et al.	1.0.8	3 years	13	3	24580	0	0
18	bio logger	Log4r wrapper with extra features for roles and	Pjotr Prins	1.0.1	6 years	4	2	23694	0	0
19	obo parser	Ruby parsering for obo files	Matt Yoder	0.4.2	7 years	5	...	23190	0	0
20	bio band	Data mining algorithms for jRuby	arrigonialberto86	0.1.11	5 years	16	3	19799	0	0
21	bio table	Swiss army knife of tabulated data; transforming/filtering tab/csv	Pjotr Prins	1.0.0	4 years	8	21	19633	0	0
22	bio alignment	Support for multiple sequence alignments (msa)	Pjotr Prins	0.1.0	14 months	11	5	19532	0	0
23	bio faster	A fast parser for fastq files	Francesco Strozzi	0.4.5	6 years	9	...	18162	0	0
24	bio vcf	Fast multi-purpose multi-threaded vcf parser	Pjotr Prins	0.9.2	2 years	54	9	16853	0	3
25	bio fastqc	Ruby parser for fastqc output	Tazro Inutano Ohta	0.10.8	4 months	2	...	16295	0	0
26	bio rocker	Rocker	Luis (Coto) Orellana, Luis M. Rodriguez-R	1.2.0	5 months			15632	0	0
27	bio basespace sdk	Basespace Ruby sdk is a Ruby based software	Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.	0.1.7	5 years	11	2	15391	0	0
28	bio dbla classifier	A tool to classify and manipulate pfemp1 dbl-alpha	George Githinji	0.7.1	5 years			15245	0	0
29	bio bigbio	Low memory sequence emitters	Pjotr Prins	0.1.6	4 years	10	1	14838	0	0
30	bio signalp	A wrapper for the signal peptide prediction algorith	Ben J Woodcroft	0.3.1	4 years	3	...	14311	0	0
31	bio phyta	Pipeline to remove contaminations from est libraries	Philipp Comans	0.9.4	7 years	2	1	14237	0	0
32	bio ngs	Bio-ngs provides a framework for handling ngs data	Francesco Strozzi, Raoul J.P. Bonnal	0.5.2	6 years	27	15	14233	0	0
33	scaffolder	Build genome output files	Michael Barton	0.5.0	5 years	7	...	13878	0	0
34	bio tm hmm	A BioRuby plugin for interaction with the transmembrane	Ben J. Woodcroft	0.2.4	20 months	2	...	13727	0	0
35	nexus parser	A nexus file format (phylogenetic inference) parser in	mjy	1.1.4	7 years	1	...	13627	0	0
36	bio kmer counter	A biogem for counting small kmers for fingerprinting	Ben J Woodcroft	0.1.2	5 years	4	...	13487	0	0
37	genevalidator	Identifying problems with gene predictions	Monica Dragan, Ismail Moghul, Anurag Priyam et al.	2.1.5	3 months	1	...	13273	0	0
38	rubyMorphbank	Simple morphbank (http://morphbank.net) services accessor	mjy	0.2.6	7 years	1	...	12490	0	0
39	bio sambamba	Ruby wrapper for sambamba tool	Artem Tarasov	0.0.5	6 years	2	...	12415	0	0
40	bio assembly	BioRuby assembly plugin	Chase Miller, Francesco Strozzi	0.1.0	7 years	4	...	12153	0	0
41	bio polymarker db batch	Server for polymarker. to be used with cron	Ricardo H. Ramirez-Gonzalez	0.5.1	3 years		...	12045	0	0
42	bio velvet	Parser to work with file formats used in	Ben J Woodcroft	0.6.0	3 years		...	12000	0	0
43	eutils	Lightweight Ruby api for ncbi eutils	Joon Lee, aka seouri	0.2.1	5 years	7	1	11907	0	0
44	taxonifi	A general purpose framework for scripted handling of development/stable	mjy	0.4.0	5 years	2	1	11824	0	0
45	bio isoelectric point	A BioRuby plugin for calculating the isoelectric point	George Githinji, Pascal Betz	0.1.3	6 years			11684	0	0
46	bio nexml	BioRuby plugin for reading and writing nexml (http://nexml.org)	Rutger Vos, Anurag Priyam	1.1.0	6 years	8	3	11541	0	0
47	bio bgzf	Reading/writing bgzf blocks	Artem Tarasov, Clayton Wheeler	0.2.1	6 years	3	...	11093	0	0
48	bioportal	Supports linking of models within a ror application	Stuart Owen, Quyen Nguyen	2.2	4 years		...	10600	0	0
49	bio genomic interval	A BioRuby plugin: handling genomic interavals and overlaps	Hiroyuki Mishima	0.1.2	7 years	4	...	10209	0	0
50	bio graphics	Library for visualizing genomic regions	Jan Aerts	1.4	10 years	23	1	10130	0	0
51	genevalidatorapp	A web app wrapper for genevalidator	Monica Dragan, Ismail Moghul, Anurag Priyam et al.	2.1.7	3 months	1	...	9481	0	0
52	bio octopus	Running and parsing of the protein transmembrane domain	Ben J Woodcroft	0.1.1	7 years	1	...	9311	0	0
53	bio cd hit report	Read and manipulate cd-hit clusters	George Githinji	0.1.0	5 years			9158	0	0
54	bio fasta retrieve	Retrieve dna sequence from ucsc using given coordinates	Andrei Rozanski	0.0.7	3 years			8993	0	0
55	bio pipengine	A pipeline manager	Francesco Strozzi, Raoul Jean Pierre Bonnal	0.9.7	15 months	17	4	8944	0	0
56	bio tabix	Ruby binding for samtools tabix	throwern	1.0.1	5 years	5	1	8935	0	0
57	bio bwa	Ruby binding for bwa mapping software	Francesco Strozzi	0.2.2	7 years	4	...	8692	0	0
58	ref2bibtex	Pass a full citation, get the bibtex back,	Matt Yoder	0.2.2	9 months		1	8556	0	1
59	bio lazyblastxml	A plugin that allows you to parse large	robsyme	0.4.0	7 years	1	...	8372	0	0
60	bio velvet underground	Bindings to some internals of the velvet assembler	Ben Woodcroft	0.3.1	2 years		1	8218	0	0
61	bio plasmoap	Implementation of the plasmoap algorithm	Ben J Woodcroft	0.1.1	2 years	1	...	8211	0	0
62	bio pileup iterator	Iterate through a samtools pileup file	Ben J. Woodcroft	0.0.4	6 years	2	...	8197	0	0
63	bio commandeer	Dead simple method of running shell commands from	Ben J. Woodcroft	0.4.0	16 months		...	8099	0	0
64	goruby	Gene ontology (go) interface for Ruby	Ben J Woodcroft	0.2.0	8 years	12	...	8003	0	0
65	bio gngm	Next-generation mapping of mutations	Dan MacLean	0.2.1	6 years	2	...	7664	0	0
66	ruby ensembl api	Api to ensembl databases	Jan Aerts, Francesco Strozzi	1.0.1	7 years	40	5	7578	0	0
67	bio statsample timeseries	Timeseries modules for statsample	Ankur Goel, Claudio Bustos	0.2.1	5 years			7570	0	0
68	publisci	Publish scientific results to the semantic web	Will Strinz	0.1.6	4 years	4	16	7528	0	0
69	bio gff3 pltools	Ruby wrapper for the gff3-pltools	Marjan Povolni	0.3.0	6 years	15	19	7475	0	0
70	bio chembl	Chembl rest api client, parser and container	Mitsuteru Nakao	0.1.3	6 years	1	1	7353	0	0
71	bio krona	This biogem is built around krona, a flashy	Ben J. Woodcroft	0.2.0	3 years	1	...	7321	0	0
72	bio ucsc util	Ruby binding to the ucsc kent utilities	throwern	0.1.2	6 years	2	...	7302	0	0
73	bio rdf	Bioinformatics triple-store support	Pjotr Prins	0.0.2	6 years	4	1	6816	0	0
74	bio affy	Parse affymetrix cel/cdf files	Pjotr Prins	0.5.1	7 years	2	1	6788	0	0
75	bio unichem	BioRuby plugin for unichem rest web service	Mitsuteru Nakao	0.3.0	5 years			6481	0	0
76	bio kb illumina	Geneexpression illuminahumanannotation	Raoul J.P. Bonnal	0.1.0	7 years	1	...	6466	0	0
77	bio liftover	Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover)	Andrei Rozanski	1.3.0	4 years	1	...	6412	0	0
78	bio synreport	Reports whether a nucleotide change results in synonymous	Dan MacLean	0.1.2	5 years		...	6398	0	0
79	bio protparam	A protparam compatible utility for BioRuby	hryk	0.2.0	5 years	2	1	5993	0	0
80	bio core	BioRuby core plugins, most and stable plugins. blastxmlparser,	Raoul J.P. Bonnal	0.0.1	7 years	1	...	5833	0	0
81	bio wolf psort wrapper	Enables the localisation predictor wolf psort to be	Ben J Woodcroft	0.0.3	6 years	1	...	5630	0	0
82	bio cnls screenscraper	Programmatic interface to the cnls nuclear localisation signal	Ben J. Woodcroft	0.3.0	6 years	2	...	5604	0	0
83	ncbi blast dbs	Fast download blast databases from ncbi beta	Anurag Priyam	0.0.6	19 months	11	3	5323	0	2
84	bio hmmer model	Parse pfam hmm definition files	Ben J. Woodcroft	0.0.2	6 years	1	...	5182	0	0
85	bio gag	Bio-gag is a biogem for detecting and correcting	Ben J Woodcroft	0.1.0	6 years	2	...	5069	0	0
86	bio biostars analytics	Biostars data-mining and statistical analysis	Joachim Baran	0.2.0	4 years			4888	0	0
87	bio locus	Fast storage and comparison of chr+pos(+alt) locations	Pjotr Prins	0.0.7	3 years	2	1	4687	0	0
88	nbio cloudquery	Client for xoopit's cloudquery api	Cameron Walters, nb.io	0.1.5	9 years	5	...	4660	0	0
89	bio sra	A sequence read archive (sra) download script and	Ben J. Woodcroft	0.3.1	2 years	3	...	4609	0	0
90	bio hmmer3 report	Enables parsing of hmmer version 3 reports	Christian Zmasek, Ben J Woodcroft	0.1.0	3 years	2	1	4315	0	0
91	bio gggenome	Gggenome Ruby client	Mitsuteru Nakao	0.2.0	5 years	1	...	4113	0	0
92	bio ensembl rest	Ruby ensembl rest api	Alberto Donizetti	0.2.0	5 years	2	...	4069	0	0
93	nbio csshttprequest	Csshttprequest is cross-domain ajax using css as a	Cameron Walters, Randy Reddig	1.0.3	9 years	91	1	3957	0	0
94	bio statsample glm	Generalized linear models for statsample	Ankur Goel	0.1.1	5 years			3952	0	0
95	rubyBHL	Rubybhl is a simple request/response wrapper for the	Matt Yoder	0.2.1	4 years	6	...	3899	0	0
96	bio mummer	Helper methods for reading .delta files	robsyme	0.2.1	3 years		...	3772	0	0
97	bio express beta diversity	Interface for express beta diversity	Ben J. Woodcroft	0.1.0	4 years		...	3732	0	0
98	bio repeatmasker	Bio-repeatmasker	Andrei Rozanski	0.0.3	4 years	1	...	3664	0	0
99	bio ipcress	A programmatic interface to the ipcress in-silico pcr	Ben J Woodcroft	0.1.0	23 months	3	...	3591	0	0
100	bio cigar	A parser for cigar format alignments	Ben J Woodcroft	0.1.0	4 years	4	...	3546	0	0
101	bio sge	BioRuby plugin for sun grid engine	Toshiaki Katayama	0.0.0	7 years	4	...	3493	0	0
102	bio samtools server	Web server for bio-samtools	homonecloco	0.1.2	4 years		...	3443	0	0
103	bio hello	Hello world plugin for the BioRuby (just for	Toshiaki Katayama	0.0.0	7 years	3	...	3438	0	0
104	bio restriction enzyme	Digests dna based on restriction enzyme cut patterns	Trevor Wennblom	1.0.0	7 years		1	3385	0	0
105	bio old biofetch emulator	Emulates as if old BioRuby biofetch alives	Naohisa Goto	1.0.0	2 years		...	3337	0	0
106	dna sequence aligner	Does high pairwise alignment of sequencing reads with	John T. Prince	0.0.2	8 years	1	...	3317	0	0
107	bio emboss six frame nucleotide sequences	A method to get the nucleotide sequence of	Ben J Woodcroft	0.1.0	7 years	1	...	3211	0	0
108	bio core ext	BioRuby core ext: plugins which require external library	Raoul J.P. Bonnal, Pjotr Prins	0.0.1	7 years	1	...	3175	0	0
109	bio biolinux	Meta package for biolinux distribution	Raoul J.P. Bonnal	0.1.0	7 years	2	...	3170	0	0
110	bio data restriction enzyme	Restriction enzyme dataset	Sir Richard J. Roberts, Trevor Wennblom	1.109.0	7 years		...	3128	0	0
111	bio ensembl	A Ruby api to the ensembl database	Jan Aerts, Francesco Strozzi	1.1.0	7 years	4	...	3128	0	0
112	bio foo	One-line summary of your gem	Toshiaki Katayama	0.0.0	7 years	1	...	3122	0	0
113	bio dbsnp	Decoding the dbsnp bitfield	Hiroyuki Mishima	0.1.1	7 years	4	...	3099	0	0
114	bio hydropathy	Hydropathy scale for BioRuby	Ben J Woodcroft	0.0.1	6 years	1	...	3066	0	0
115	bio phyloxml	Phyloxml plugin for BioRuby	Diana Jaunzeikare, Clayton Wheeler	0.9.0	6 years	3	1	3046	0	0
116	bio exportpred	Wrapper around the exportpred algorithm for predicting p	Ben J Woodcroft	0.0.1	6 years	1	...	3042	0	0
117	intermine bio	Biological extensions for the intermine webservice client library	Alex Kalderimis	0.98.1	7 years	1	...	3037	0	0
118	bio aliphatic index	A simple biogem that allows computation of the	Ben J Woodcroft	0.0.1	6 years	1	...	3035	0	0
119	bio incanter	Build graph with jRuby	Matteo Picciolini	0.1.0	6 years			2965	0	0
120	bio img metadata	Reads metadata from integrated microbial genomes (img) metadata	Ben J. Woodcroft	0.0.1	5 years		...	2628	0	0
121	bio gfastqc	Aggregate fastqc (quality control for next generation sequencing	Raoul Jean Pierre Bonnal	0.0.4	3 years		...	2592	0	0
122	bio freebayes	The api for freebayes version #{bio::freebayes::extversion}	Natapol Pornputtapong	0.1.6	3 years			2529	0	0
123	bio stockholm	Parse stockholm sequence alignment format	Ben J. Woodcroft	0.0.1	5 years	2	...	2473	0	0
124	bio raxml	Ruby wrapper to run standard-raxml for maximum likelihood	Fernando Izquierdo	0.1.0	5 years		...	2361	0	0
125	bio kseq	Ruby inferface for kseq.h by heng li for	Fedor Gusev	0.0.2	4 years	1	...	2167	0	0
126	bio exominer	Mine publications for gene names	Pjotr Prins	0.0.3	4 years	2	...	1971	0	0
127	bark	A Ruby wrapper on the open tree api beta	Matt Yoder	0.0.2	4 years	1	...	1883	0	0
128	genomichdt	A restful service for sharing genomic data	Joachim Baran, Robert Buels, Michel Dumontier	0.0.1	4 years			1812	0	0
129	bio faidx	Tools to work with fasta files, indexed with	homonecloco	0.0.1	4 years		...	1805	0	0
130	bio gemma wrapper	gemma with loco and permutations	Pjotr Prins	0.98.1	3 weeks		...	1779	1	7
131	bio blat tools	Tools to manipulate blat files from the command	homonecloco	0.1.0	4 years		...	1772	0	0
132	bio location rdfize	Faldo location output method for bio::location in BioRuby	Joachim Baran, Naohisa Goto	0.0.0	4 years		...	1737	0	0
133	bio picard	Api of picard tool	Natapol Pornputtapong	1.131.5	3 years			1653	0	0
134	bio sparql client	A Ruby wrapper for bio sparql service	Natapol Pornputtapong	0.0.1	3 years			1597	0	0
135	nbio css http request	Csshttprequest is cross-domain ajax using css disabled	Cameron Walters, Randy Reddig	0.1	9 years			1549	0	0
136	bio jaspar	Tools for jaspar motifs in BioRuby	Jessica Lee, Wasserman Lab	0.1.0	3 years		...	1377	0	0
137	bio kallisto	Basic wrapper for the kallistio mapper	homonecloco	0.1.0	3 years	1	...	1371	0	0
138	bio conduit	A pipeline creator for BioRuby	Natapol Pornputtapong	1.0.0	3 years			1367	0	0
139	bio plates	Methods for handling multiwell plate annotations	Steve Pettitt	0.2.0	2 years		...	1191	0	0
140	bio sam mutation	Parsing and mutation calling from sam, cigar and	Stephen Pettitt	0.4.1	2 years		1	1131	0	0
141	bio biosql	Biosql plugin for BioRuby	BioRuby project	0.0.0	2 years		...	915	0	0
142	bio shell	BioRuby shell: interactive analysis environment for BioRuby	BioRuby project	0.0.0	15 months		...	511	0	0
143	bio executables	BioRuby executables: utilities bundled with BioRuby	BioRuby project	0.0.0	15 months		...	504	0	0
144	bio primer3	pre		pre			...	0	0	0

*) gem downloads (total & last 90 days) from rubygems.org as of 2018-12-11
**) number of commits on GitHub (last 7 days & last 90 days)